A high-resolution survey of deletion polymorphism in the human genome

Recent work has shown that copy number polymorphism is an important class of genetic variation in human genomes. Here we report a new method that uses SNP genotype data from parent-offspring trios to identify polymorphic deletions. We applied this method to data from the International HapMap Project to produce the first high-resolution population surveys of deletion polymorphism. Approximately 100 of these deletions have been experimentally validated using comparative genome hybridization on tiling-resolution oligonucleotide microarrays. Our analysis identifies a total of 586 distinct regions that harbor deletion polymorphisms in one or more of the families. Notably, we estimate that typical individuals are hemizygous for roughly 30-50 deletions larger than 5 kb, totaling around 550-750 kb of euchromatic sequence across their genomes. The detected deletions span a total of 267 known and predicted genes. Overall, however, the deleted regions are relatively gene-poor, consistent with the action of purifying selection against deletions. Deletion polymorphisms may well have an important role in the genetics of complex traits; however, they are not directly observed in most current gene mapping studies. Our new method will permit the identification of deletion polymorphisms in high-density SNP surveys of trio or other family data.     

The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome

We determined the complete genome sequence of Clostridium difficile strain 630, a virulent and multidrug-resistant strain. Our analysis indicates that a large proportion (11%) of the genome consists of mobile genetic elements, mainly in the form of conjugative transposons. These mobile elements are putatively responsible for the acquisition by C. difficile of an extensive array of genes involved in antimicrobial resistance, virulence, host interaction and the production of surface structures. The metabolic capabilities encoded in the genome show multiple adaptations for survival and growth within the gut environment. The extreme genome variability was confirmed by whole-genome microarray analysis; it may reflect the organism's niche in the gut and should provide information on the evolution of virulence in this organism.     

Germline rates of de novo meiotic deletions and duplications causing several genomic disorders

Meiotic recombination between highly similar duplicated sequences (nonallelic homologous recombination, NAHR) generates deletions, duplications, inversions and translocations, and it is responsible for genetic diseases known as 'genomic disorders', most of which are caused by altered copy number of dosage-sensitive genes. NAHR hot spots have been identified within some duplicated sequences. We have developed sperm-based assays to measure the de novo rate of reciprocal deletions and duplications at four NAHR hot spots. We used these assays to dissect the relative rates of NAHR between different pairs of duplicated sequences. We show that (i) these NAHR hot spots are specific to meiosis, (ii) deletions are generated at a higher rate than their reciprocal duplications in the male germline and (iii) some of these genomic disorders are likely to have been underascertained clinically, most notably that resulting from the duplication of 7q11, the reciprocal of the deletion causing Williams-Beuren syndrome.     

Bioadsorption of 4-Chlorophenol to the Activated Sludge

IntroductionChlorinated phenolic compounds,which aregenerated from a number of industrialmanufacturing processes,comprise the bulk of theenvironmental pollutants.Aqueous effluents fromindustrial operations such as polymeric resinproduction,oil refining,iron- steel,petroleum,pesticide,paint,solvent,pharmaceutics,woodpreserving chemicals,coke- oven,and paper andpulp industries contain chlorophenolic compounds.Their fate in the environment is of greatimportance as they are toxic,recalcitrant andb…     

Forecasting with growth curves: the effect of error structure

"The main theme of this paper is an investigation into the importance of error structure as a determinant of the forecasting accuracy of the logistic model. The relationship between the variance of the disturbance term and forecasting accuracy is examined empirically. A general local logistic model is developed as a vehicle to be used in this investigation. Some brief comments are made on the assumptions about error structure, implicit or explicit, in the literature." The results suggest that "the variance of the disturbance term, when using the logistic to forecast human populations, is proportional to at least the square of population size."     

ADVANCES IN SUSTAINABLE SECURITY SYSTEMS ENGINEERING WITH DRAMA THEORY （DT） II

We put forth Drama Theory II (DT II) as a formal multiple participant decision making framework that can be used to systematically model complex security challenges, and advance the field of Sustainable Security Systems Engineering. DT II is defined as a theory of “large world” pre-game communication and equilibrium selection. While game theoretic tools have been widely applied to resolve environmental conflicts and promote global security, traditional game theory assumes that decision makers, options, and preferences are fixed. A mathematical treatment of key drama theoretic concepts (i.e. positions, intentions, doubts and dilemmas) is provided. The dynamics of the drama theoretic process are discussed and the expected equilibrium set is derived. The fundamental theorem of drama theory is proven and all theoretical results are applied to promote sustainable security solutions. It is emphasized that DT II represents a flexible systems engineering technique to address time-sensitive, multi-faceted, and complex multiple participant negotiations.     

Scattering by chorus waves as the dominant cause of diffuse auroral precipitation

Earth's diffuse aurora occurs over a broad latitude range and is primarily caused by the precipitation of low-energy (0.1-30-keV) electrons originating in the central plasma sheet, which is the source region for hot electrons in the nightside outer magnetosphere. Although generally not visible, the diffuse auroral precipitation provides the main source of energy for the high-latitude nightside upper atmosphere, leading to enhanced ionization and chemical changes. Previous theoretical studies have indicated that two distinct classes of magnetospheric plasma wave, electrostatic electron cyclotron harmonic waves and whistler-mode chorus waves, could be responsible for the electron scattering that leads to diffuse auroral precipitation, but it has hitherto not been possible to determine which is the more important. Here we report an analysis of satellite wave data and Fokker-Planck diffusion calculations which reveals that scattering by chorus is the dominant cause of the most intense diffuse auroral precipitation. This resolves a long-standing controversy. Furthermore, scattering by chorus can remove most electrons as they drift around Earth's magnetosphere, leading to the development of observed pancake distributions, and can account for the global morphology of the diffuse aurora.     

Effective leadership and decision-making in animal groups on the move

For animals that forage or travel in groups, making movement decisions often depends on social interactions among group members. However, in many cases, few individuals have pertinent information, such as knowledge about the location of a food source, or of a migration route. Using a simple model we show how information can be transferred within groups both without signalling and when group members do not know which individuals, if any, have information. We reveal that the larger the group the smaller the proportion of informed individuals needed to guide the group, and that only a very small proportion of informed individuals is required to achieve great accuracy. We also demonstrate how groups can make consensus decisions, even though informed individuals do not know whether they are in a majority or minority, how the quality of their information compares with that of others, or even whether there are any other informed individuals. Our model provides new insights into the mechanisms of effective leadership and decision-making in biological systems.